Announcements

Last year's Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted. Continue reading →

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of … Continue reading →

BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . - This is mainly a bug fix release addressing issues with the protein structure and disorder modules - One … Continue reading →

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading →

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading →

About BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

Getting BioJava

BioJava is distributed under the terms of the GNU Lesser GPL. This means that you can use the libraries without your software being forced under either the LGPL or GPL. LGPL is not GPL.

BioJava releases can be obtained from our download area. Instructions for installing the library, and building source releases, can be found on the Getting started page.

You can also maintain an up-to-date view of BioJava with CVS. Additionally, we provide an anonymous CVS server.

If you wish to contribute your existing code or help maintain part of the BioJava code-base, then we can supply you with a read/write account. Sign up for the biojava-dev mailing list and post a request for an account.

BioJava 1.5 Release Planning

BioJava 1.5-Beta2 is now available from the download area. --Mark 01:39, 29 December 2006 (EST)

Planning has begun for a new BioJava release. The release plan has been drawn up. Soon we will be asking for a volunteer to be the Release Czar to oversee the coordination of the release.

Bugs and Requests for enhancement

BioJava probably contains the odd bug, who would have thought!! We make use of the Bugzilla bug reporting and tracking system. You can use it to submit a new bug or request for enhancement or to view open bugs or known issues.

Documentation

Cookbook

The biojava project maintains a cookbook of examples that help you perform common tasks and get you started using biojava. The cookbook is affectionately known as Biojava in Anger. A French version is also available.

API Documentation (JavaDocs)

The following are links to API documentation autogenerated by javadoc.

Dazzle

The Dazzle DAS server repository and documentation has been moved to a new location

Thanks

The open-bio servers reside in in a Tier 1 Boston area colocation
facility.
Infrastructure geeks can see pictures of the colocation cage and the
new OBF servers online at this URL:
[1] -- those servers also host
EMBOSS FTP/CVS and mailing lists.

We would like to thank Chris Dagdigian from The Bioteam for providing and maintaining the bio* servers.